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Cottonseed oil, soft in taste and golden in color, plays a crucial role in various foods. In addition, cottonseed oil has attracted much attention due to its unique fatty acid properties, anti-inflammatory and heart protective properties. Therefore, it is of great significance to understand the genetic mechanism that regulates the biosynthesis of cottonseed storage oil, carry out key gene mining, and select high-quality cotton varieties with high oil content. With the rapid development of high-throughput sequencing technology and bioinformatics analysis tools, whole genome sequencing has become simpler and more efficient, genome-wide association analysis (GWAS) has become a key tool for studying complex traits. This paper introduces the principle and research advantages of GWAS, discusses the progress of its application in the research of different oil crops and cotton characters. Some suggestions for future genetic studies of cottonseed oil related traits were put forward. The existing problems were discussed and prospected in order to provide a theoretical basis for future studies on the genetic basis of cottonseed oil traits and marker-assisted breeding by GWAS. [ABSTRACT FROM AUTHOR]